FLOW CYTOMETRY – DATA COMPRESSION A.E. Bras PhD Student Erasmus University, Rotterdam, the Netherlands
Flow Cytometry
Flow Cytometry
Flow Cytometry
Flow Cytometry
Flow Cytometry
Flow Cytometry
Older Systems
Older Systems
Newer Systems
Newer Systems
Newer Systems
Newer Systems FLOATING POINT DATA - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Newer Systems FLOATING POINT DATA - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - MILLIONS - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Storage FLOATING POINT DATA - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - MILLIONS - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Storage .FCS FLOATING POINT DATA - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - MILLIONS - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Storage FLOW CYTOMETRY STRANDARD .FCS FLOATING POINT DATA - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - MILLIONS - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Storage FLOW CYTOMETRY STRANDARD .FCS PRO WIDELEY USED FLOATING POINT DATA - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - MILLIONS - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Storage FLOW CYTOMETRY STRANDARD .FCS PRO WIDELEY USED FLOATING POINT DATA - - - - - - - - - - - - CON - - - - - - - - - - - - NO COMPRESSION - - - - - - - - - - - - MILLIONS - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Lossless Compression .FCS
Lossless Compression .FCS ≈ 70 % .ZIP
Lossless Compression .FCS ≈ 70 % .ZIP Better alternative?
Lossless Compression - Benchmark
Lossless Compression - Benchmark .FCS 167.131
Lossless Compression - Benchmark RANDOM .FCS 167.131
Lossless Compression - Benchmark RANDOM .FCS 167.131
Lossless Compression - Benchmark CODEC RATIO CODEC RATIO LZIP 0.533 ZPAQ 0.460 LZMA 0.533 BCM 0.510 XZ 0.533 LZIP 0.533 GLZA 0.558 LZMA 0.533 LZHAM 0.568 FLZMA2 0.539 CSC 0.590 LZHAM 0.569 BROTLI 0.598 BROTLI 0.571 TORNADO 0.622 BZIP2 0.580 ZSTD 0.626 CSC 0.590 XPACK 0.637 BALZ 0.598 ZLING 0.665 XPACK 0.612 LIBDEFLATE 0.676 ZSTD 0.625 LZFSE 0.690 ZOPFLI 0.674 RANDOM CRUSH 0.692 LIBDEFLATE 0.676 ZLIB 0.695 LZFSE 0.690 UCL_NRV2D 0.725 CRUSH 0.692 UCL_NRV2E 0.725 ZLIB 0.695 UCL_NRV2B 0.734 BRIEFLZ 0.727 LZO1X 0.755 DOBOZ 0.750 LZO1Z 0.757 LZSSE8 0.758 LZSSE8 0.758 BSCQLFC 0.763 LZO1Y 0.768 LZSSE2 0.768 LZSSE2 0.768 LZ4 0.777 LIZARD 0.770 LZSSE4 0.781 DENSITY 0.771 LZG 0.803 .FCS LZO2A 0.774 SUBOTIN 0.819 LZO1B 0.775 FASTAC 0.819 LZ4HC 0.777 ZLIBH 0.823 167.131 ... ... ... ...
Lossless Compression - Benchmark CODEC RATIO CODEC RATIO LZIP 0.533 ZPAQ 0.460 LZMA 0.533 BCM 0.510 XZ 0.533 LZIP 0.533 GLZA 0.558 LZMA 0.533 LZHAM 0.568 FLZMA2 0.539 CSC 0.590 LZHAM 0.569 BROTLI 0.598 BROTLI 0.571 TORNADO 0.622 BZIP2 0.580 ZSTD 0.626 CSC 0.590 XPACK 0.637 BALZ 0.598 ZLING 0.665 XPACK 0.612 LIBDEFLATE 0.676 ZSTD 0.625 LZFSE 0.690 ZOPFLI 0.674 RANDOM CRUSH 0.692 LIBDEFLATE 0.676 ZLIB 0.695 LZFSE 0.690 UCL_NRV2D 0.725 CRUSH 0.692 UCL_NRV2E 0.725 ZLIB 0.695 UCL_NRV2B 0.734 BRIEFLZ 0.727 LZO1X 0.755 DOBOZ 0.750 LZO1Z 0.757 LZSSE8 0.758 LZSSE8 0.758 BSCQLFC 0.763 LZO1Y 0.768 LZSSE2 0.768 LZSSE2 0.768 LZ4 0.777 LIZARD 0.770 LZSSE4 0.781 DENSITY 0.771 LZG 0.803 .FCS LZO2A 0.774 SUBOTIN 0.819 LZO1B 0.775 FASTAC 0.819 LZ4HC 0.777 ZLIBH 0.823 167.131 ... ... ... ...
Lossless Compression - Benchmark CODEC RATIO CODEC RATIO LZIP 0.533 ZPAQ 0.460 LZMA 0.533 BCM 0.510 XZ 0.533 LZIP 0.533 GLZA 0.558 LZMA 0.533 LZHAM 0.568 FLZMA2 0.539 CSC 0.590 LZHAM 0.569 BROTLI 0.598 BROTLI 0.571 TORNADO 0.622 BZIP2 0.580 ZSTD 0.626 CSC 0.590 XPACK 0.637 BALZ 0.598 ZLING 0.665 XPACK 0.612 LIBDEFLATE 0.676 ZSTD 0.625 LZFSE 0.690 ZOPFLI 0.674 CRUSH 0.692 LIBDEFLATE 0.676 ZLIB 0.695 LZFSE 0.690 UCL_NRV2D 0.725 CRUSH 0.692 UCL_NRV2E 0.725 ZLIB 0.695 UCL_NRV2B 0.734 BRIEFLZ 0.727 LZO1X 0.755 DOBOZ 0.750 LZO1Z 0.757 LZSSE8 0.758 LZSSE8 0.758 BSCQLFC 0.763 LZO1Y 0.768 LZSSE2 0.768 LZSSE2 0.768 LZ4 0.777 LIZARD 0.770 LZSSE4 0.781 DENSITY 0.771 LZG 0.803 .FCS LZO2A 0.774 SUBOTIN 0.819 LZO1B 0.775 FASTAC 0.819 LZ4HC 0.777 ZLIBH 0.823 167.131 ... ... ... ...
Lossless Compression - Benchmark
Lossless Compression - Benchmark ≈ 0.45
Implementation in R
Implementation in R base::memCompress(type=" XZ ")
Implementation in R base::memCompress(type=" XZ ")
Bioconductor - flowCore
Bioconductor - flowCore
Bioconductor - flowCore C:\input.fcs flowCore::read.FCS flowSom::FlowSOM flowCore::write.FCS C:\output.fcs
Bioconductor - flowCore base::readBin C:\input.fcs flowCore::read.FCS flowSom::FlowSOM flowCore::write.FCS C:\output.fcs
Bioconductor - flowCore base::readBin C:\input.fcs flowCore::read.FCS flowSom::FlowSOM flowCore::write.FCS base::writeBin C:\output.fcs
Bioconductor - flowCore base::readBin C:\input.fcs flowCore::read.FCS flowSom::FlowSOM flowCore::write.FCS base::memCompress base::writeBin C:\output.fcs
Bioconductor - flowCore base::readBin C:\input.fcs base::memDecompress flowCore::read.FCS flowSom::FlowSOM flowCore::write.FCS base::memCompress base::writeBin C:\output.fcs
Bioconductor - flowCore C:\input.fcs flowCore::read.FCS flowSom::FlowSOM flowCore::write.FCS .TAR.GZ C:\output.fcs
Bioconductor - flowCore C:\input.fcs flowCore::read.FCS flowSom::FlowSOM flowCore::write.FCS .TAR.GZ C:\output.fcs
Bioconductor - flowCore C:\input.fcs flowCore::read.FCS flowSom::FlowSOM flowCore::write.FCS .TAR.GZ C:\output.fcs
Bioconductor - flowCore C:\input.fcs flowCore::read.FCS flowSom::FlowSOM flowCore::write.FCS .FCS.XZ C:\output.fcs
Bioconductor - flowCore C:\input.fcs flowCore::read.FCS flowSom::FlowSOM flowCore::write.FCS .FCS.XZ C:\output.fcs
Bioconductor - flowCore C:\input.fcs flowCore::read.FCS flowSom::FlowSOM flowCore::write.FCS .FCS.XZ C:\output.fcs
Bioconductor - flowCore C:\input.fcs flowCore::read.FCS flowSom::FlowSOM flowCore::write.FCS .FCS.XZ C:\output.fcs
Bioconductor – flowCore - Pipelines
Bioconductor – flowCore - Pipeline C:\input\01.fcs C:\input\02.fcs flowCore::read.flowSet flowCore::write.flowSet C:\output\01.fcs C:\output\02.fcs
Bioconductor – flowCore - Pipeline C:\input.zip base::unzip C:\input\01.fcs C:\input\02.fcs flowCore::read.flowSet flowCore::write.flowSet C:\output\01.fcs C:\output\02.fcs
Bioconductor – flowCore - Pipeline C:\input.zip base::unzip C:\input\01.fcs C:\input\02.fcs flowCore::read.flowSet flowCore::write.flowSet C:\output\01.fcs C:\output\02.fcs base::zip C:\output.zip
Bioconductor – flowCore - Pipeline C:\input.zip base::unzip C:\input\01.fcs C:\input\02.fcs flowCore::read.flowSet flowCore::write.flowSet C:\output\01.fcs C:\output\02.fcs base::zip C:\output.zip
Bioconductor – flowCore - Pipeline C:\input.zip base::unzip C:\input\01.fcs C:\input\02.fcs flowCore::read.flowSet ARCHIVAL flowCore::write.flowSet CYTOMETRY STANDARD C:\output\01.fcs C:\output\02.fcs .ACS base::zip C:\output.zip
Bioconductor – flowCore - Pipeline = ARCHIVAL CYTOMETRY STANDARD .ACS .ZIP
Bioconductor – flowCore - Pipeline = ARCHIVAL CYTOMETRY .FCS .FCS .FCS STANDARD .ACS .ZIP
Bioconductor – flowCore - Pipeline .TXT = ARCHIVAL CYTOMETRY .FCS .FCS .FCS STANDARD .ACS .ZIP
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